메뉴 건너뛰기




Volumn 7, Issue 6, 2012, Pages

Local structural differences in homologous proteins: Specificities in different SCOP classes

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84862671752     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038805     Document Type: Article
Times cited : (13)

References (114)
  • 1
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker D, Sali A, (2001) Protein structure prediction and structural genomics. Science 294: 93-96.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 2
    • 38849098884 scopus 로고    scopus 로고
    • Acyl carrier protein: structure-function relationships in a conserved multifunctional protein family
    • Byers DM, Gong H, (2007) Acyl carrier protein: structure-function relationships in a conserved multifunctional protein family. Biochem Cell Biol 85: 649-662.
    • (2007) Biochem Cell Biol , vol.85 , pp. 649-662
    • Byers, D.M.1    Gong, H.2
  • 3
    • 33749014910 scopus 로고    scopus 로고
    • Evolution of protein structural classes and protein sequence families
    • Choi IG, Kim SH, (2006) Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci U S A 103: 14056-14061.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 14056-14061
    • Choi, I.G.1    Kim, S.H.2
  • 4
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C, Lesk AM, (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5: 823-826.
    • (1986) EMBO J , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 5
    • 0027485083 scopus 로고
    • Comparison of conformational characteristics in structurally similar protein pairs
    • Flores TP, Orengo CA, Moss DS, Thornton JM, (1993) Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci 2: 1811-1826.
    • (1993) Protein Sci , vol.2 , pp. 1811-1826
    • Flores, T.P.1    Orengo, C.A.2    Moss, D.S.3    Thornton, J.M.4
  • 6
    • 41949103740 scopus 로고    scopus 로고
    • The structure of protein evolution and the evolution of protein structure
    • Goldstein RA, (2008) The structure of protein evolution and the evolution of protein structure. Curr Opin Struct Biol 18: 170-177.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 170-177
    • Goldstein, R.A.1
  • 7
    • 0035783063 scopus 로고    scopus 로고
    • Fold change in evolution of protein structures
    • Grishin NV, (2001) Fold change in evolution of protein structures. J Struct Biol 134: 167-185.
    • (2001) J Struct Biol , vol.134 , pp. 167-185
    • Grishin, N.V.1
  • 10
    • 0002929101 scopus 로고
    • A model of evolutionary change in proteins
    • Eck, Washington D.C: National Biomedical Research Foundation
    • Dayhoff MO, Eck RV, Eck (1972) A model of evolutionary change in proteins. Atlas of protein sequence and structure. Washington D.C: National Biomedical Research Foundation.
    • (1972) Atlas of protein sequence and structure
    • Dayhoff, M.O.1    Eck, R.V.2
  • 11
    • 0026656815 scopus 로고
    • Exhaustive matching of the entire protein sequence database
    • Gonnet GH, Cohen MA, Benner SA, (1992) Exhaustive matching of the entire protein sequence database. Science 256: 1443-1445.
    • (1992) Science , vol.256 , pp. 1443-1445
    • Gonnet, G.H.1    Cohen, M.A.2    Benner, S.A.3
  • 12
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM, (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8: 275-282.
    • (1992) Comput Appl Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 13
    • 0031805465 scopus 로고    scopus 로고
    • Assessing the impact of secondary structure and solvent accessibility on protein evolution
    • Goldman N, Thorne JL, Jones DT, (1998) Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149: 445-458.
    • (1998) Genetics , vol.149 , pp. 445-458
    • Goldman, N.1    Thorne, J.L.2    Jones, D.T.3
  • 14
    • 0025997601 scopus 로고
    • Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities
    • Luthy R, McLachlan AD, Eisenberg D, (1991) Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins 10: 229-239.
    • (1991) Proteins , vol.10 , pp. 229-239
    • Luthy, R.1    McLachlan, A.D.2    Eisenberg, D.3
  • 15
    • 0025104478 scopus 로고
    • Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction
    • Overington J, Johnson MS, Sali A, Blundell TL, (1990) Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc Biol Sci 241: 132-145.
    • (1990) Proc Biol Sci , vol.241 , pp. 132-145
    • Overington, J.1    Johnson, M.S.2    Sali, A.3    Blundell, T.L.4
  • 16
    • 0029985399 scopus 로고    scopus 로고
    • Combining protein evolution and secondary structure
    • Thorne JL, Goldman N, Jones DT, (1996) Combining protein evolution and secondary structure. Mol Biol Evol 13: 666-673.
    • (1996) Mol Biol Evol , vol.13 , pp. 666-673
    • Thorne, J.L.1    Goldman, N.2    Jones, D.T.3
  • 17
    • 0027439391 scopus 로고
    • Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables
    • Topham CM, McLeod A, Eisenmenger F, Overington JP, Johnson MS, et al. (1993) Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables. J Mol Biol 229: 194-220.
    • (1993) J Mol Biol , vol.229 , pp. 194-220
    • Topham, C.M.1    McLeod, A.2    Eisenmenger, F.3    Overington, J.P.4    Johnson, M.S.5
  • 18
    • 0028304961 scopus 로고
    • Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. II. Secondary structures
    • Wako H, Blundell TL, (1994) Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. II. Secondary structures. J Mol Biol 238: 693-708.
    • (1994) J Mol Biol , vol.238 , pp. 693-708
    • Wako, H.1    Blundell, T.L.2
  • 19
    • 0028239337 scopus 로고
    • Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. I. Solvent accessibility classes
    • Wako H, Blundell TL, (1994) Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. I. Solvent accessibility classes. J Mol Biol 238: 682-692.
    • (1994) J Mol Biol , vol.238 , pp. 682-692
    • Wako, H.1    Blundell, T.L.2
  • 20
    • 0033056948 scopus 로고    scopus 로고
    • A protein taxonomy based on secondary structure
    • Przytycka T, Aurora R, Rose GD, (1999) A protein taxonomy based on secondary structure. Nat Struct Biol 6: 672-682.
    • (1999) Nat Struct Biol , vol.6 , pp. 672-682
    • Przytycka, T.1    Aurora, R.2    Rose, G.D.3
  • 21
    • 27544439433 scopus 로고    scopus 로고
    • Evolutionary plasticity of protein families: coupling between sequence and structure variation
    • Panchenko AR, Wolf YI, Panchenko LA, Madej T, (2005) Evolutionary plasticity of protein families: coupling between sequence and structure variation. Proteins 61: 535-544.
    • (2005) Proteins , vol.61 , pp. 535-544
    • Panchenko, A.R.1    Wolf, Y.I.2    Panchenko, L.A.3    Madej, T.4
  • 22
    • 2442637669 scopus 로고    scopus 로고
    • The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint
    • Castillo-Davis CI, Kondrashov FA, Hartl DL, Kulathinal RJ, (2004) The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. Genome Res 14: 802-811.
    • (2004) Genome Res , vol.14 , pp. 802-811
    • Castillo-Davis, C.I.1    Kondrashov, F.A.2    Hartl, D.L.3    Kulathinal, R.J.4
  • 23
    • 0345070506 scopus 로고    scopus 로고
    • Mutational equilibrium model of genome size evolution
    • Petrov DA, (2002) Mutational equilibrium model of genome size evolution. Theor Popul Biol 61: 531-544.
    • (2002) Theor Popul Biol , vol.61 , pp. 531-544
    • Petrov, D.A.1
  • 24
    • 64049085201 scopus 로고    scopus 로고
    • Length variations amongst protein domain superfamilies and consequences on structure and function
    • Sandhya S, Rani SS, Pankaj B, Govind MK, Offmann B, et al. (2009) Length variations amongst protein domain superfamilies and consequences on structure and function. PLoS One 4: e4981.
    • (2009) PLoS One , vol.4
    • Sandhya, S.1    Rani, S.S.2    Pankaj, B.3    Govind, M.K.4    Offmann, B.5
  • 25
    • 0036601353 scopus 로고    scopus 로고
    • Trends in protein evolution inferred from sequence and structure analysis
    • Aravind L, Mazumder R, Vasudevan S, Koonin EV, (2002) Trends in protein evolution inferred from sequence and structure analysis. Curr Opin Struct Biol 12: 392-399.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 392-399
    • Aravind, L.1    Mazumder, R.2    Vasudevan, S.3    Koonin, E.V.4
  • 26
    • 38849191693 scopus 로고    scopus 로고
    • Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions
    • Jiang H, Blouin C, (2007) Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions. BMC Bioinformatics 8: 444.
    • (2007) BMC Bioinformatics , vol.8 , pp. 444
    • Jiang, H.1    Blouin, C.2
  • 27
    • 0029130841 scopus 로고
    • The emerging role of insertions and deletions in protein engineering
    • Shortle D, Sondek J, (1995) The emerging role of insertions and deletions in protein engineering. Curr Opin Biotechnol 6: 387-393.
    • (1995) Curr Opin Biotechnol , vol.6 , pp. 387-393
    • Shortle, D.1    Sondek, J.2
  • 28
    • 0025339507 scopus 로고
    • Accommodation of single amino acid insertions by the native state of staphylococcal nuclease
    • Sondek J, Shortle D, (1990) Accommodation of single amino acid insertions by the native state of staphylococcal nuclease. Proteins 7: 299-305.
    • (1990) Proteins , vol.7 , pp. 299-305
    • Sondek, J.1    Shortle, D.2
  • 29
    • 1842717956 scopus 로고    scopus 로고
    • Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes
    • Taylor MS, Ponting CP, Copley RR, (2004) Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes. Genome Res 14: 555-566.
    • (2004) Genome Res , vol.14 , pp. 555-566
    • Taylor, M.S.1    Ponting, C.P.2    Copley, R.R.3
  • 30
    • 0026566796 scopus 로고
    • Analysis of insertions/deletions in protein structures
    • Pascarella S, Argos P, (1992) Analysis of insertions/deletions in protein structures. J Mol Biol 224: 461-471.
    • (1992) J Mol Biol , vol.224 , pp. 461-471
    • Pascarella, S.1    Argos, P.2
  • 31
    • 77955103653 scopus 로고    scopus 로고
    • Systematic analysis of short internal indels and their impact on protein folding
    • Kim R, Guo JT, (2010) Systematic analysis of short internal indels and their impact on protein folding. BMC Struct Biol 10: 24.
    • (2010) BMC Struct Biol , vol.10 , pp. 24
    • Kim, R.1    Guo, J.T.2
  • 32
    • 3342888069 scopus 로고    scopus 로고
    • Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments
    • Chang MS, Benner SA, (2004) Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments. J Mol Biol 341: 617-631.
    • (2004) J Mol Biol , vol.341 , pp. 617-631
    • Chang, M.S.1    Benner, S.A.2
  • 33
    • 78650491535 scopus 로고    scopus 로고
    • Impact of indels on the flanking regions in structural domains
    • Zhang Z, Huang J, Wang Z, Wang L, Gao P, (2011) Impact of indels on the flanking regions in structural domains. Mol Biol Evol 28: 291-301.
    • (2011) Mol Biol Evol , vol.28 , pp. 291-301
    • Zhang, Z.1    Huang, J.2    Wang, Z.3    Wang, L.4    Gao, P.5
  • 35
  • 36
    • 0017709445 scopus 로고
    • Beta-turns in proteins
    • Chou PY, Fasman GD, (1977) Beta-turns in proteins. J Mol Biol 115: 135-175.
    • (1977) J Mol Biol , vol.115 , pp. 135-175
    • Chou, P.Y.1    Fasman, G.D.2
  • 37
    • 0015114095 scopus 로고
    • Folding of polypeptide chains in proteins: a proposed mechanism for folding
    • Lewis PN, Momany FA, Scheraga HA, (1971) Folding of polypeptide chains in proteins: a proposed mechanism for folding. Proc Natl Acad Sci U S A 68: 2293-2297.
    • (1971) Proc Natl Acad Sci U S A , vol.68 , pp. 2293-2297
    • Lewis, P.N.1    Momany, F.A.2    Scheraga, H.A.3
  • 38
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • Richardson JS, (1981) The anatomy and taxonomy of protein structure. Adv Protein Chem 34: 167-339.
    • (1981) Adv Protein Chem , vol.34 , pp. 167-339
    • Richardson, J.S.1
  • 39
    • 0030596522 scopus 로고    scopus 로고
    • Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding
    • Yang AS, Hitz B, Honig B, (1996) Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding. J Mol Biol 259: 873-882.
    • (1996) J Mol Biol , vol.259 , pp. 873-882
    • Yang, A.S.1    Hitz, B.2    Honig, B.3
  • 40
    • 0032900496 scopus 로고    scopus 로고
    • Prediction of the location and type of beta-turns in proteins using neural networks
    • Shepherd AJ, Gorse D, Thornton JM, (1999) Prediction of the location and type of beta-turns in proteins using neural networks. Protein Sci 8: 1045-1055.
    • (1999) Protein Sci , vol.8 , pp. 1045-1055
    • Shepherd, A.J.1    Gorse, D.2    Thornton, J.M.3
  • 41
    • 77955078003 scopus 로고    scopus 로고
    • Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures
    • Kountouris P, Hirst JD, (2010) Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures. BMC Bioinformatics 11: 407.
    • (2010) BMC Bioinformatics , vol.11 , pp. 407
    • Kountouris, P.1    Hirst, J.D.2
  • 42
    • 0030039296 scopus 로고    scopus 로고
    • PROMOTIF-a program to identify and analyze structural motifs in proteins
    • Hutchinson EG, Thornton JM, (1996) PROMOTIF-a program to identify and analyze structural motifs in proteins. Protein Sci 5: 212-220.
    • (1996) Protein Sci , vol.5 , pp. 212-220
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 43
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 44
    • 0034669774 scopus 로고    scopus 로고
    • Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks
    • de Brevern AG, Etchebest C, Hazout S, (2000) Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins 41: 271-287.
    • (2000) Proteins , vol.41 , pp. 271-287
    • de Brevern, A.G.1    Etchebest, C.2    Hazout, S.3
  • 45
    • 0022701772 scopus 로고
    • Using known substructures in protein model building and crystallography
    • Jones TA, Thirup S, (1986) Using known substructures in protein model building and crystallography. EMBO J 5: 819-822.
    • (1986) EMBO J , vol.5 , pp. 819-822
    • Jones, T.A.1    Thirup, S.2
  • 46
    • 0036406112 scopus 로고    scopus 로고
    • Small libraries of protein fragments model native protein structures accurately
    • Kolodny R, Koehl P, Guibas L, Levitt M, (2002) Small libraries of protein fragments model native protein structures accurately. J Mol Biol 323: 297-307.
    • (2002) J Mol Biol , vol.323 , pp. 297-307
    • Kolodny, R.1    Koehl, P.2    Guibas, L.3    Levitt, M.4
  • 47
    • 0026754015 scopus 로고
    • Accurate modeling of protein conformation by automatic segment matching
    • Levitt M, (1992) Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 226: 507-533.
    • (1992) J Mol Biol , vol.226 , pp. 507-533
    • Levitt, M.1
  • 48
    • 0034284383 scopus 로고    scopus 로고
    • Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies
    • Micheletti C, Seno F, Maritan A, (2000) Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies. Proteins 40: 662-674.
    • (2000) Proteins , vol.40 , pp. 662-674
    • Micheletti, C.1    Seno, F.2    Maritan, A.3
  • 49
    • 0025326949 scopus 로고
    • Automatic definition of recurrent local structure motifs in proteins
    • Rooman MJ, Rodriguez J, Wodak SJ, (1990) Automatic definition of recurrent local structure motifs in proteins. J Mol Biol 213: 327-336.
    • (1990) J Mol Biol , vol.213 , pp. 327-336
    • Rooman, M.J.1    Rodriguez, J.2    Wodak, S.J.3
  • 50
    • 0029860175 scopus 로고    scopus 로고
    • Local structural motifs of protein backbones are classified by self-organizing neural networks
    • Schuchhardt J, Schneider G, Reichelt J, Schomburg D, Wrede P, (1996) Local structural motifs of protein backbones are classified by self-organizing neural networks. Protein Eng 9: 833-842.
    • (1996) Protein Eng , vol.9 , pp. 833-842
    • Schuchhardt, J.1    Schneider, G.2    Reichelt, J.3    Schomburg, D.4    Wrede, P.5
  • 51
    • 0024395940 scopus 로고
    • A 3D building blocks approach to analyzing and predicting structure of proteins
    • Unger R, Harel D, Wherland S, Sussman JL, (1989) A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins 5: 355-373.
    • (1989) Proteins , vol.5 , pp. 355-373
    • Unger, R.1    Harel, D.2    Wherland, S.3    Sussman, J.L.4
  • 52
    • 33144460796 scopus 로고    scopus 로고
    • Local protein structure prediction using discriminative models
    • Sander O, Sommer I, Lengauer T, (2006) Local protein structure prediction using discriminative models. BMC Bioinformatics 7: 14.
    • (2006) BMC Bioinformatics , vol.7 , pp. 14
    • Sander, O.1    Sommer, I.2    Lengauer, T.3
  • 53
    • 33947434131 scopus 로고    scopus 로고
    • Analycys: a database for conservation and conformation of disulphide bonds in homologous protein domains
    • Thangudu RR, Sharma P, Srinivasan N, Offmann B, (2007) Analycys: a database for conservation and conformation of disulphide bonds in homologous protein domains. Proteins 67: 255-261.
    • (2007) Proteins , vol.67 , pp. 255-261
    • Thangudu, R.R.1    Sharma, P.2    Srinivasan, N.3    Offmann, B.4
  • 54
    • 23144437382 scopus 로고    scopus 로고
    • New assessment of a structural alphabet
    • de Brevern AG, (2005) New assessment of a structural alphabet. In Silico Biol 5: 283-289.
    • (2005) In Silico Biol , vol.5 , pp. 283-289
    • de Brevern, A.G.1
  • 56
    • 18844454820 scopus 로고    scopus 로고
    • A structural alphabet for local protein structures: improved prediction methods
    • Etchebest C, Benros C, Hazout S, de Brevern AG, (2005) A structural alphabet for local protein structures: improved prediction methods. Proteins 59: 810-827.
    • (2005) Proteins , vol.59 , pp. 810-827
    • Etchebest, C.1    Benros, C.2    Hazout, S.3    de Brevern, A.G.4
  • 57
    • 54249084066 scopus 로고    scopus 로고
    • LOCUSTRA: accurate prediction of local protein structure using a two-layer support vector machine approach
    • Zimmermann O, Hansmann UH, (2008) LOCUSTRA: accurate prediction of local protein structure using a two-layer support vector machine approach. J Chem Inf Model 48: 1903-1908.
    • (2008) J Chem Inf Model , vol.48 , pp. 1903-1908
    • Zimmermann, O.1    Hansmann, U.H.2
  • 58
    • 44949123664 scopus 로고    scopus 로고
    • Analysis and prediction of protein local structure based on structure alphabets
    • Dong Q, Wang X, Lin L, Wang Y, (2008) Analysis and prediction of protein local structure based on structure alphabets. Proteins 72: 163-172.
    • (2008) Proteins , vol.72 , pp. 163-172
    • Dong, Q.1    Wang, X.2    Lin, L.3    Wang, Y.4
  • 59
    • 57749200715 scopus 로고    scopus 로고
    • Analyzing the sequence-structure relationship of a library of local structural prototypes
    • Benros C, de Brevern AG, Hazout S, (2009) Analyzing the sequence-structure relationship of a library of local structural prototypes. J Theor Biol 256: 215-226.
    • (2009) J Theor Biol , vol.256 , pp. 215-226
    • Benros, C.1    de Brevern, A.G.2    Hazout, S.3
  • 60
    • 33947526348 scopus 로고    scopus 로고
    • "Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence
    • de Brevern AG, Etchebest C, Benros C, Hazout S, (2007) "Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence. J Biosci 32: 51-70.
    • (2007) J Biosci , vol.32 , pp. 51-70
    • de Brevern, A.G.1    Etchebest, C.2    Benros, C.3    Hazout, S.4
  • 61
    • 61449129495 scopus 로고    scopus 로고
    • Fragment-based local statistical potentials derived by combining an alphabet of protein local structures with secondary structures and solvent accessibilities
    • Li Q, Zhou C, Liu H, (2009) Fragment-based local statistical potentials derived by combining an alphabet of protein local structures with secondary structures and solvent accessibilities. Proteins 74: 820-836.
    • (2009) Proteins , vol.74 , pp. 820-836
    • Li, Q.1    Zhou, C.2    Liu, H.3
  • 62
    • 68949178663 scopus 로고    scopus 로고
    • Protein short loop prediction in terms of a structural alphabet
    • Tyagi M, Bornot A, Offmann B, de Brevern AG, (2009) Protein short loop prediction in terms of a structural alphabet. Comput Biol Chem 33: 329-333.
    • (2009) Comput Biol Chem , vol.33 , pp. 329-333
    • Tyagi, M.1    Bornot, A.2    Offmann, B.3    de Brevern, A.G.4
  • 63
    • 70449359175 scopus 로고    scopus 로고
    • Protein local 3D structure prediction by Super Granule Support Vector Machines (Super GSVM)
    • Chen B, Johnson M, (2009) Protein local 3D structure prediction by Super Granule Support Vector Machines (Super GSVM). BMC Bioinformatics 10: S15.
    • (2009) BMC Bioinformatics , vol.10
    • Chen, B.1    Johnson, M.2
  • 64
    • 34147202792 scopus 로고    scopus 로고
    • Discovering structural motifs using a structural alphabet: application to magnesium-binding sites
    • Dudev M, Lim C, (2007) Discovering structural motifs using a structural alphabet: application to magnesium-binding sites. BMC Bioinformatics 8: 106.
    • (2007) BMC Bioinformatics , vol.8 , pp. 106
    • Dudev, M.1    Lim, C.2
  • 65
    • 65749097053 scopus 로고    scopus 로고
    • Analysis of protein contacts into Protein Units
    • Faure G, Bornot A, de Brevern AG, (2009) Analysis of protein contacts into Protein Units. Biochimie 91: 876-887.
    • (2009) Biochimie , vol.91 , pp. 876-887
    • Faure, G.1    Bornot, A.2    de Brevern, A.G.3
  • 68
    • 70349333875 scopus 로고    scopus 로고
    • Using reduced amino acid composition to predict defensin family and subfamily: Integrating similarity measure and structural alphabet
    • Zuo YC, Li QZ, (2009) Using reduced amino acid composition to predict defensin family and subfamily: Integrating similarity measure and structural alphabet. Peptides 30: 1788-1793.
    • (2009) Peptides , vol.30 , pp. 1788-1793
    • Zuo, Y.C.1    Li, Q.Z.2
  • 70
    • 84888702947 scopus 로고    scopus 로고
    • Local Structure Alphabets
    • In: Rangwala H, Karypis G, editors, editors
    • Joseph AP, Bornot A, de Brevern AG, (2010) Local Structure Alphabets. In: Rangwala H, Karypis G, editors. editors. Protein Structure Prediction John Wiley & Sons, Inc., Hoboken, NJ, USA.
    • (2010)
    • Joseph, A.P.1    Bornot, A.2    de Brevern, A.G.3
  • 71
    • 77955814959 scopus 로고    scopus 로고
    • A structural-alphabet-based strategy for finding structural motifs across protein families
    • Wu CY, Chen YC, Lim C, (2010) A structural-alphabet-based strategy for finding structural motifs across protein families. Nucleic Acids Res 38: e150.
    • (2010) Nucleic Acids Res , vol.38
    • Wu, C.Y.1    Chen, Y.C.2    Lim, C.3
  • 72
    • 33747831751 scopus 로고    scopus 로고
    • Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet
    • Tyagi M, Sharma P, Swamy CS, Cadet F, Srinivasan N, et al. (2006) Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. Nucleic Acids Res 34: W119-123.
    • (2006) Nucleic Acids Res , vol.34
    • Tyagi, M.1    Sharma, P.2    Swamy, C.S.3    Cadet, F.4    Srinivasan, N.5
  • 73
    • 33748280492 scopus 로고    scopus 로고
    • A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications
    • Tyagi M, Gowri VS, Srinivasan N, de Brevern AG, Offmann B, (2006) A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications. Proteins 65: 32-39.
    • (2006) Proteins , vol.65 , pp. 32-39
    • Tyagi, M.1    Gowri, V.S.2    Srinivasan, N.3    de Brevern, A.G.4    Offmann, B.5
  • 74
    • 79959930240 scopus 로고    scopus 로고
    • Improvement of protein structure comparison using a structural alphabet
    • Joseph AP, Srinivasan N, de Brevern AG, (2011) Improvement of protein structure comparison using a structural alphabet. Biochimie 93: 1434-1445.
    • (2011) Biochimie , vol.93 , pp. 1434-1445
    • Joseph, A.P.1    Srinivasan, N.2    de Brevern, A.G.3
  • 75
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C, (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 76
    • 85083121798 scopus 로고    scopus 로고
    • Self-Organizing Maps (3rd edition): Springer
    • Kohonen T, (2001) Self-Organizing Maps (3rd edition): Springer. 501 p.
    • (2001) 501 P
    • Kohonen, T.1
  • 77
    • 79959981766 scopus 로고    scopus 로고
    • iPBA: a tool for protein structure comparison using sequence alignment strategies
    • Gelly JC, Joseph AP, Srinivasan N, de Brevern AG, (2011) iPBA: a tool for protein structure comparison using sequence alignment strategies. Nucleic Acids Res 39: W18-23.
    • (2011) Nucleic Acids Res , vol.39
    • Gelly, J.C.1    Joseph, A.P.2    Srinivasan, N.3    de Brevern, A.G.4
  • 78
    • 0035175268 scopus 로고    scopus 로고
    • PALI-a database of Phylogeny and ALIgnment of homologous protein structures
    • Balaji S, Sujatha S, Kumar SS, Srinivasan N, (2001) PALI-a database of Phylogeny and ALIgnment of homologous protein structures. Nucleic Acids Res 29: 61-65.
    • (2001) Nucleic Acids Res , vol.29 , pp. 61-65
    • Balaji, S.1    Sujatha, S.2    Kumar, S.S.3    Srinivasan, N.4
  • 79
    • 0037246028 scopus 로고    scopus 로고
    • Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database
    • Gowri VS, Pandit SB, Karthik PS, Srinivasan N, Balaji S, (2003) Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. Nucleic Acids Res 31: 486-488.
    • (2003) Nucleic Acids Res , vol.31 , pp. 486-488
    • Gowri, V.S.1    Pandit, S.B.2    Karthik, P.S.3    Srinivasan, N.4    Balaji, S.5
  • 80
    • 0035011451 scopus 로고    scopus 로고
    • PALI: a database of alignments and phylogeny of homologous protein structures
    • Sujatha S, Balaji S, Srinivasan N, (2001) PALI: a database of alignments and phylogeny of homologous protein structures. Bioinformatics 17: 375-376.
    • (2001) Bioinformatics , vol.17 , pp. 375-376
    • Sujatha, S.1    Balaji, S.2    Srinivasan, N.3
  • 82
    • 0027361123 scopus 로고
    • A structural basis for sequence comparisons. An evaluation of scoring methodologies
    • Johnson MS, Overington JP, (1993) A structural basis for sequence comparisons. An evaluation of scoring methodologies. J Mol Biol 233: 716-738.
    • (1993) J Mol Biol , vol.233 , pp. 716-738
    • Johnson, M.S.1    Overington, J.P.2
  • 83
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith TF, Waterman MS, (1981) Identification of common molecular subsequences. J Mol Biol 147: 195-197.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 84
    • 0031825181 scopus 로고    scopus 로고
    • Obligatory steps in protein folding and the conformational diversity of the transition state
    • Martinez JC, Pisabarro MT, Serrano L, (1998) Obligatory steps in protein folding and the conformational diversity of the transition state. Nat Struct Biol 5: 721-729.
    • (1998) Nat Struct Biol , vol.5 , pp. 721-729
    • Martinez, J.C.1    Pisabarro, M.T.2    Serrano, L.3
  • 85
    • 33947315642 scopus 로고    scopus 로고
    • Secondary structure assignment that accurately reflects physical and evolutionary characteristics
    • Cubellis MV, Cailliez F, Lovell SC, (2005) Secondary structure assignment that accurately reflects physical and evolutionary characteristics. BMC Bioinformatics 6: S8.
    • (2005) BMC Bioinformatics , vol.6
    • Cubellis, M.V.1    Cailliez, F.2    Lovell, S.C.3
  • 86
    • 0003742069 scopus 로고
    • Department of Biochemistry and Molecular Biology, University College London. pp Computer Program
    • Hubbard SJ, Thornton JM, (1993) NACCESS. Department of Biochemistry and Molecular Biology, University College London. pp. Computer Program.
    • (1993) NACCESS
    • Hubbard, S.J.1    Thornton, J.M.2
  • 87
    • 0032545165 scopus 로고    scopus 로고
    • Conformational interconversions in peptide beta-turns: analysis of turns in proteins and computational estimates of barriers
    • Gunasekaran K, Gomathi L, Ramakrishnan C, Chandrasekhar J, Balaram P, (1998) Conformational interconversions in peptide beta-turns: analysis of turns in proteins and computational estimates of barriers. J Mol Biol 284: 1505-1516.
    • (1998) J Mol Biol , vol.284 , pp. 1505-1516
    • Gunasekaran, K.1    Gomathi, L.2    Ramakrishnan, C.3    Chandrasekhar, J.4    Balaram, P.5
  • 89
    • 0027988868 scopus 로고
    • The T-to-R transformation in hemoglobin: a reevaluation
    • Srinivasan R, Rose GD, (1994) The T-to-R transformation in hemoglobin: a reevaluation. Proc Natl Acad Sci U S A 91: 11113-11117.
    • (1994) Proc Natl Acad Sci U S A , vol.91 , pp. 11113-11117
    • Srinivasan, R.1    Rose, G.D.2
  • 90
    • 0034769527 scopus 로고    scopus 로고
    • Peptide-plane flipping in proteins
    • Hayward S, (2001) Peptide-plane flipping in proteins. Protein Sci 10: 2219-2227.
    • (2001) Protein Sci , vol.10 , pp. 2219-2227
    • Hayward, S.1
  • 91
    • 0028566270 scopus 로고
    • A revised set of potentials for beta-turn formation in proteins
    • Hutchinson EG, Thornton JM, (1994) A revised set of potentials for beta-turn formation in proteins. Protein Sci 3: 2207-2216.
    • (1994) Protein Sci , vol.3 , pp. 2207-2216
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 92
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L, Sander C, (1993) Protein structure comparison by alignment of distance matrices. J Mol Biol 233: 123-138.
    • (1993) J Mol Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 94
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov IN, Bourne PE, (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11: 739-747.
    • (1998) Protein Eng , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 95
    • 48249130416 scopus 로고    scopus 로고
    • Novel protein folds and their nonsequential structural analogs
    • Guerler A, Knapp EW, (2008) Novel protein folds and their nonsequential structural analogs. Protein Sci 17: 1374-1382.
    • (2008) Protein Sci , vol.17 , pp. 1374-1382
    • Guerler, A.1    Knapp, E.W.2
  • 96
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: a protein structure alignment algorithm based on the TM-score
    • Zhang Y, Skolnick J, (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33: 2302-2309.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 97
    • 3042581007 scopus 로고    scopus 로고
    • Flexible structure alignment by chaining aligned fragment pairs allowing twists
    • Ye Y, Godzik A, (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19: ii246-255.
    • (2003) Bioinformatics , vol.19
    • Ye, Y.1    Godzik, A.2
  • 99
    • 0027367977 scopus 로고
    • Helix capping propensities in peptides parallel those in proteins
    • Chakrabartty A, Doig AJ, Baldwin RL, (1993) Helix capping propensities in peptides parallel those in proteins. Proc Natl Acad Sci U S A 90: 11332-11336.
    • (1993) Proc Natl Acad Sci U S A , vol.90 , pp. 11332-11336
    • Chakrabartty, A.1    Doig, A.J.2    Baldwin, R.L.3
  • 100
    • 26444611841 scopus 로고    scopus 로고
    • Alpha-alpha linking motifs and interhelical orientations
    • Engel DE, DeGrado WF, (2005) Alpha-alpha linking motifs and interhelical orientations. Proteins 61: 325-337.
    • (2005) Proteins , vol.61 , pp. 325-337
    • Engel, D.E.1    DeGrado, W.F.2
  • 101
    • 0036180675 scopus 로고    scopus 로고
    • A test of proposed rules for helix capping: implications for protein design
    • Sagermann M, Martensson LG, Baase WA, Matthews BW, (2002) A test of proposed rules for helix capping: implications for protein design. Protein Sci 11: 516-521.
    • (2002) Protein Sci , vol.11 , pp. 516-521
    • Sagermann, M.1    Martensson, L.G.2    Baase, W.A.3    Matthews, B.W.4
  • 104
    • 0031038377 scopus 로고    scopus 로고
    • Local interactions in protein folding: lessons from the alpha-helix
    • Aurora R, Creamer TP, Srinivasan R, Rose GD, (1997) Local interactions in protein folding: lessons from the alpha-helix. J Biol Chem 272: 1413-1416.
    • (1997) J Biol Chem , vol.272 , pp. 1413-1416
    • Aurora, R.1    Creamer, T.P.2    Srinivasan, R.3    Rose, G.D.4
  • 105
    • 1842591839 scopus 로고    scopus 로고
    • Kinetic role of helix caps in protein folding is context-dependent
    • Kapp GT, Richardson JS, Oas TG, (2004) Kinetic role of helix caps in protein folding is context-dependent. Biochemistry 43: 3814-3823.
    • (2004) Biochemistry , vol.43 , pp. 3814-3823
    • Kapp, G.T.1    Richardson, J.S.2    Oas, T.G.3
  • 106
    • 0032553332 scopus 로고    scopus 로고
    • Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters
    • Lacroix E, Viguera AR, Serrano L, (1998) Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. J Mol Biol 284: 173-191.
    • (1998) J Mol Biol , vol.284 , pp. 173-191
    • Lacroix, E.1    Viguera, A.R.2    Serrano, L.3
  • 107
    • 33646567807 scopus 로고    scopus 로고
    • Lifting the lid on helix-capping
    • Rose GD, (2006) Lifting the lid on helix-capping. Nat Chem Biol 2: 123-124.
    • (2006) Nat Chem Biol , vol.2 , pp. 123-124
    • Rose, G.D.1
  • 108
    • 27144489108 scopus 로고    scopus 로고
    • Protein database searches using compositionally adjusted substitution matrices
    • Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, et al. (2005) Protein database searches using compositionally adjusted substitution matrices. FEBS J 272: 5101-5109.
    • (2005) FEBS J , vol.272 , pp. 5101-5109
    • Altschul, S.F.1    Wootton, J.C.2    Gertz, E.M.3    Agarwala, R.4    Morgulis, A.5
  • 109
    • 44649194987 scopus 로고    scopus 로고
    • A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins
    • Brick K, Pizzi E, (2008) A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins. BMC Bioinformatics 9: 236.
    • (2008) BMC Bioinformatics , vol.9 , pp. 236
    • Brick, K.1    Pizzi, E.2
  • 110
    • 33646259688 scopus 로고    scopus 로고
    • Composition-modified matrices improve identification of homologs of saccharomyces cerevisiae low-complexity glycoproteins
    • Coronado JE, Attie O, Epstein SL, Qiu WG, Lipke PN, (2006) Composition-modified matrices improve identification of homologs of saccharomyces cerevisiae low-complexity glycoproteins. Eukaryot Cell 5: 628-637.
    • (2006) Eukaryot Cell , vol.5 , pp. 628-637
    • Coronado, J.E.1    Attie, O.2    Epstein, S.L.3    Qiu, W.G.4    Lipke, P.N.5
  • 111
    • 16344388556 scopus 로고    scopus 로고
    • The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions
    • Yu YK, Altschul SF, (2005) The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions. Bioinformatics 21: 902-911.
    • (2005) Bioinformatics , vol.21 , pp. 902-911
    • Yu, Y.K.1    Altschul, S.F.2
  • 112
    • 57149085484 scopus 로고    scopus 로고
    • Genome bias influences amino acid choices: analysis of amino acid substitution and re-compilation of substitution matrices exclusive to an AT-biased genome
    • Paila U, Kondam R, Ranjan A, (2008) Genome bias influences amino acid choices: analysis of amino acid substitution and re-compilation of substitution matrices exclusive to an AT-biased genome. Nucleic Acids Res 36: 6664-6675.
    • (2008) Nucleic Acids Res , vol.36 , pp. 6664-6675
    • Paila, U.1    Kondam, R.2    Ranjan, A.3
  • 113
    • 38449088265 scopus 로고    scopus 로고
    • Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays
    • Ellrott K, Guo JT, Olman V, Xu Y, (2007) Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays. Comput Syst Bioinformatics Conf 6: 335-342.
    • (2007) Comput Syst Bioinformatics Conf , vol.6 , pp. 335-342
    • Ellrott, K.1    Guo, J.T.2    Olman, V.3    Xu, Y.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.